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"Walter, Ryan"
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ATRX restricts Human Cytomegalovirus (HCMV) viral DNA replication through heterochromatinization and minimizes unpackaged viral genomes
ATRX limits the accumulation of human cytomegalovirus (HCMV) Immediate Early (IE) proteins at the start of productive, lytic infections, and thus is a part of the cell-intrinsic defenses against infecting viruses. ATRX is a chromatin remodeler and a component of a histone chaperone complex. Therefore, we hypothesized ATRX would inhibit the transcription of HCMV IE genes by increasing viral genome heterochromatinization and decreasing its accessibility. To test this hypothesis, we quantitated viral transcription and genome structure in cells replete with or depleted of ATRX. We found ATRX did indeed limit viral IE transcription, increase viral genome chromatinization, and decrease viral genome accessibility. The inhibitory effects of ATRX extended to Early (E) and Late (L) viral protein accumulation, viral DNA replication, and progeny virion output. However, we found the negative effects of ATRX on HCMV viral DNA replication were independent of its effects on viral IE and E protein accumulation but correlated with viral genome heterochromatinization. Interestingly, the increased number of viral genomes synthesized in ATRX-depleted cells were not efficiently packaged, indicating the ATRX-mediated restriction to HCMV viral DNA replication may benefit productive infection by increasing viral fitness. Our work mechanistically describes the antiviral function of ATRX and introduces a novel, pro-viral role for this protein, perhaps explaining why, unlike during infections with other herpesviruses, it is not directly targeted by a viral countermeasure in HCMV infected cells.
Journal Article
Effects of basin-scale climate modes and upwelling on nearshore marine heatwaves and cold spells in the California Current
Marine heatwaves and cold spells (MHWs/MCSs) have been observed to be increasing globally in frequency and intensity based on satellite remote sensing and continue to pose a major threat to marine ecosystems worldwide. Despite this, there are limited in-situ based observational studies in the very shallow nearshore region, particularly in Eastern Boundary Current Upwelling Systems (EBUS). We analyzed a unique dataset collected in shallow waters along central California spanning more than four decades (1978–2020) and assessed links with basin-scale climate modes [Pacific Decadal Oscillation (PDO) and El Niño (MEI)] and regional-scale wind-driven upwelling. We found no significant increase/decrease in MHW/MCS frequency, duration, or intensity over the last four decades, but did observe considerable interannual variability linked with basin-scale climate modes. Additionally, there was a decrease in both MHW/MCS occurrence during the upwelling season, and the initiation of individual MHWs/MCSs coincided with anomalous upwelling. Most notably, the co-occurrence of warm (cold) phases of the PDO and MEI with negative (positive) upwelling anomalies strongly enhanced the relative frequency of positive (negative) temperature anomalies and MHW (MCS) days. Collectively, both basin-scale variability and upwelling forcing play a key role in predicting extreme events and shaping nearshore resilience in EBUS.
Journal Article
High resolution assessment of commercial fisheries activity along the US West Coast using Vessel Monitoring System data with a case study using California groundfish fisheries
Commercial fisheries along the US West Coast are important components of local and regional economies. They use various fishing gear, target a high diversity of species, and are highly spatially heterogeneous, making it challenging to generate a synoptic picture of fisheries activity in the region. Still, understanding the spatial and temporal dynamics of US West Coast fisheries is critical to meet the US legal mandate to manage fisheries sustainably and to better coordinate activities among a growing number of users of ocean space, including offshore renewable energy, aquaculture, shipping, and interactions with habitats and key non-fishery species such as seabirds and marine mammals. We analyzed vessel tracking data from Vessel Monitoring System (VMS) from 2010 to 2017 to generate high-resolution spatio-temporal estimates of contemporary fishing effort across a wide range of commercial fisheries along the entire US West Coast. We identified over 247,000 fishing trips across the entire VMS data, covering over 25 different fisheries. We validated the spatial accuracy of our analyses using independent estimates of spatial groundfish fisheries effort generated through the NOAA’s National Marine Fisheries Service Observer Program. Additionally, for commercial groundfish fisheries operating in federal waters in California, we combined the VMS data with landings and ex-vessel value data from California commercial fisheries landings receipts to generate highly resolved estimates of landings and ex-vessel value, matching over 38,000 fish tickets with VMS data that included 87% of the landings and 76% of the ex-vessel value for groundfish. We highlight fisheries-specific and spatially-resolved patterns of effort, landings, and ex-vessel value, a bimodal distribution of fishing effort with respect to depth, and variable and generally declining effort over eight years. The information generated by our study can help inform future sustainable spatial fisheries management and other activities in the marine environment including offshore renewable energy planning.
Journal Article
Climate change and variability drive increasing exposure of marine heatwaves across US estuaries
Marine heatwaves (MHWs) are among the greatest threats to marine ecosystems, and while substantial advances have been made in oceanic MHWs, little is known about estuarine MHWs. Utilizing a temperature dataset spanning over two decades and 54 stations distributed across 20 estuaries in the United States National Estuarine Research Reserve System, we present a comprehensive analysis of estuarine MHW characteristics and trends. Long-term climate-change-driven warming is driving more frequent MHWs along the East Coast, and if trends continue, this region will be in a MHW state for ~ 1/3 of the year by the end of the century. In contrast, the vast majority of the West Coast showed no trends, highlighting the potential for future thermal refugia. The West Coast was more strongly influenced by climate variability through the enhancement/suppression of MHWs during different phases of climate modes, suggesting long-term predictability potential. These results can provide guidance for management actions and planning in these critical environments.
Journal Article
Application of Deep Learning for Classification of Intertidal Eelgrass from Drone-Acquired Imagery
Shallow estuarine habitats are globally undergoing rapid changes due to climate change and anthropogenic influences, resulting in spatiotemporal shifts in distribution and habitat extent. Yet, scientists and managers do not always have rapidly available data to track habitat changes in real-time. In this study, we apply a novel and a state-of-the-art image segmentation machine learning technique (DeepLab) to two years of high-resolution drone-based imagery of a marine flowering plant species (eelgrass, a temperate seagrass). We apply the model to eelgrass (Zostera marina) meadows in the Morro Bay estuary, California, an estuary that has undergone large eelgrass declines and the subsequent recovery of seagrass meadows in the last decade. The model accurately classified eelgrass across a range of conditions and sizes from meadow-scale to small-scale patches that are less than a meter in size. The model recall, precision, and F1 scores were 0.954, 0.723, and 0.809, respectively, when using human-annotated training data and random assessment points. All our accuracy values were comparable to or demonstrated greater accuracy than other models for similar seagrass systems. This study demonstrates the potential for advanced image segmentation machine learning methods to accurately support the active monitoring and analysis of seagrass dynamics from drone-based images, a framework likely applicable to similar marine ecosystems globally, and one that can provide quantitative and accurate data for long-term management strategies that seek to protect these vital ecosystems.
Journal Article
Marine Heatwave Co‐Occurrence Between Estuarine and Coastal Systems
Marine heatwaves (MHWs), prolonged periods of anomalously warm ocean temperatures, pose significant threats to marine ecosystems. While MHWs in coastal and estuarine systems have been studied separately, their spatial coherence remains significantly understudied. Here we analyze over 2 decades of high‐frequency in situ temperature data from 54 stations across 20 U.S. estuaries and 13 coastal buoys to assess MHW co‐occurrences. We find that estuarine and coastal MHWs co‐occur only ∼21% of the time, a 57% decrease compared to co‐occurrence within estuaries (∼49%). Maximum co‐occurrence occurs at zero lag, suggesting synchronous synoptic‐scale atmospheric forcing, likely via air–sea heat fluxes. Co‐occurrence shows strong seasonality, peaking in fall and weakening in summer, and declines exponentially with distance, with an e‐folding scale O(100 km), consistent with synoptic‐scale atmospheric forcing. This study offers the most comprehensive assessment to date of estuarine‐coastal MHW co‐occurrence and offers a baseline for understanding and forecasting these extreme events.
Journal Article
THE ENTHUSIASM OF DAVID RICARDO
Britons viewed speculative thinking as a primary cause of the French Revolution and the disorders that followed. In this context, Edmund Burke and others identified a form of enthusiasm that was theoretical, not religious, in nature, but which also corrupted reasoning to disastrous effect. This article investigates how this accusation was made against David Ricardo and his political economy, and the variable defences that he deployed. The result is to uncover the language that was used to appraise political economy in the late eighteenth and early nineteenth centuries, along with the intellectual disciplines that were prescribed to protect economic reasoning from falling into fantasy.
Journal Article
Seasonal and interannual variability of phytoplankton abundance and community composition on the Central Coast of California
Variations in the abundance and composition of phytoplankton greatly impact ecosystem structure and function. Within the California Current System (CCS), phytoplankton community structure is tightly coupled to seasonal variability in wind-driven coastal upwelling, a process that drives changes in coastal water temperatures and nutrient concentrations. Based on approximately a decade (2008–2018) of weekly phytoplankton measurements, this study provides the first characterization of the seasonal and interannual variability of phytoplankton abundance and composition in San Luis Obispo (SLO) Bay, an understudied region within the CCS. Overall, the seasonality of phytoplankton in SLO Bay mirrored that of the larger CCS; diatoms dominated the community during the spring upwelling season, whereas dinoflagellates dominated the community during the fall relaxation period. While we observed considerable interannual variability among phytoplankton taxa, of particular note was the absence of a fall dinoflagellate-dominated period from 2010 through 2013, followed by the return of the fall dinoflagellate-dominated period in 2014. This compositional shift coincided with a major phase shift of both the Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO). In addition to exerting a strong influence on the seasonality of phytoplankton community succession and transition between diatom- and dinoflagellate-dominated periods, the state of both the PDO and NPGO also influenced the extent to which environmental conditions (temperature and upwelling winds) could predict community type. These results highlight the importance of long-term datasets and the consideration of large-scale climate patterns when assessing local ecosystem dynamics.
Journal Article